Modern Japanese people arose from 3 ancestral groups, 1 of them unknown, DNA study suggests

Image of a crowd of people crossing the Shibuya intersection. One set of white marking lines can be seen running parallel to the bottom side of the image, while another run diagonally towards the upper left-hand corner of the image. A range of people can be seen crossing from those carrying backpacks, others carrying shopping bags, some dressed in suits and others in jeans
A large new study has revealed new insight into the evolutionary history of Japanese people. (Image credit: Grant Faint via Getty Images)

Modern Japanese people largely descend from three ancestral groups, a new study suggests. The research also reveals genetic ties with our closest extinct relatives — the Neanderthals and Denisovans — and how these genes may affect present-day disease risk. 

In one of the largest non-European analyses of its kind, scientists sequenced the DNA of more than 3,200 Japanese people across seven regions of the country, extending from the snowy mountains of Hokkaido in the north to the subtropical southern shores of Okinawa. 

The researchers collated these genetic data, along with relevant clinical information, into a large new database called the Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL).

The team discovered that modern Japanese people mostly descended from three ancestral groups: Neolithic Jomon hunter-gatherers; a group believed to have been the ancient predecessors of the Han Chinese; and an unidentified group with ties to Northeast Asia. This finding further challenges a contested, three-decades-long hypothesis that Japanese people originated from the Jomon people and, later, rice-farming Yayoi migrants from continental Asia.

Related: India's evolutionary past tied to huge migration 50,000 years ago and to now-extinct human relatives

The new analysis also revealed 42 pieces of DNA that Japanese people inherited from Neanderthals and two from Denisovans that could be linked to complex traits, meaning those that are encoded by multiple genes. This inheritance was likely the result of earlier interbreeding events between these ancient groups and early Homo sapiens, the authors wrote in the paper. 

Denisovan-derived DNA within a gene called NKX6-1 was associated with the development of type 2 diabetes (T2D), and within the gene POLR3E, it was tied to height, the authors found. Eleven Neanderthal-derived DNA sequences were found to be associated with seven diseases, including T2D, coronary artery disease, prostate cancer and the inflammatory disorder rheumatoid arthritis. Most of these 44 chunks of ancient DNA are unique to East Asians, the authors said. 

Until recently, large-scale genetic sequencing research has focused on analyzing DNA from people of European descent, leaving a significant gap in our understanding of other human populations, including those in Asia. Therefore, the new findings may provide some long-coveted answers.

"This comprehensive genetic dataset enables us to delve into uncharted territories concerning population and medical genetics of the Japanese population," the authors wrote in a paper describing their findings, published Wednesday (April 17) in the journal Science Advances

These discoveries could even supplement research that could lead to the development of personalized medicine, the authors wrote. 

For instance, the team identified gene mutations that could be clinically important within the Japanese population. One notable example is a mutation in a gene called PTPRD that was found in six people in the cohort. Clinical information was available for three of these individuals, who experienced several of the same health conditions, including having heart attacks, kidney failure and high blood pressure. 

JEWEL will serve as a "reference for future genetic research within and beyond the Japanese population," the study authors concluded.

Emily Cooke
Staff Writer

Emily is a health news writer based in London, United Kingdom. She holds a bachelor's degree in biology from Durham University and a master's degree in clinical and therapeutic neuroscience from Oxford University. She has worked in science communication, medical writing and as a local news reporter while undertaking journalism training. In 2018, she was named one of MHP Communications' 30 journalists to watch under 30. (